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DAXX envelops a histone H3.3–H4 dimer for H3.3-specific recognition

Nature volume 491, pages 560–565 (2012)Cite this article

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Abstract

Histone chaperones represent a structurally and functionally diverse family of histone-binding proteins that prevent promiscuous interactions of histones before their assembly into chromatin. DAXX is a metazoan histone chaperone specific to the evolutionarily conserved histone variant H3.3. Here we report the crystal structures of the DAXX histone-binding domain with a histone H3.3–H4 dimer, including mutants within DAXX and H3.3, together with in vitro and in vivo functional studies that elucidate the principles underlying H3.3 recognition specificity. Occupying 40% of the histone surface-accessible area, DAXX wraps around the H3.3–H4 dimer, with complex formation accompanied by structural transitions in the H3.3–H4 histone fold. DAXX uses an extended α-helical conformation to compete with major inter-histone, DNA and ASF1 interaction sites. Our structural studies identify recognition elements that read out H3.3-specific residues, and functional studies address the contributions of Gly 90 in H3.3 and Glu 225 in DAXX to chaperone-mediated H3.3 variant recognition specificity.

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Figure 1: Structure of the ternary complex of DAXX histone-binding domain (HBD, 178-389) bound to histones H3.3 and H4, and comparison with the ternary HJURP–CENPA–H4 complex.
Figure 2: DAXX competes with major DNA interactions sites and prevents histone tetramer formation through conformational changes in H3.3.
Figure 3: DAXX uses an extended α-helical conformation to compete with ASF1 interaction sites.
Figure 4: A structural role for H3.3 G90 as the major determinant for H3.3 variant specificity of DAXX in vivo.
Figure 5: The DAXX tower provides H3.3 G90 specificity through direct and water-mediated contacts with H3.3 αN, α1 and α2 helices.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic structures of the DAXX–H3.3–H4 complex have been deposited in the RCSB Protein Data Bank with accession codes 4H9N (five-substituent native complex at 1.95A˚ ), 4H9S (seven-substituent native complex at 2.60A˚ ), 4H9O (five-substituent H3.3(G90M) mutant complex at 2.05A˚ ), 4H9P (five-substituent H3.3(G90A) mutant complex at 2.20A˚ ), 4H9Q (five-substituent DAXX(E225A) mutant complex at 1.95A˚ ) and 4H9R (five-substituent DAXX(E225A)–H3.3(G90A) mutant complex at 2.20A˚ ). Supplementary Video 1 shows the ternary five-substituent native complex of DAXX–H3.3–H4.

Change history

  • 21 November 2012

    A change was made to the title.

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Acknowledgements

We thank the personnel of synchrotron beam lines 24-I/D-C/E at the Advanced Photon Source (Argonne National Laboratory) and beam line X29 at the Brookhaven National Laboratory for their assistance, and the Center for Synchrotron Biosciences grant, P30-EB-009998, from the National Institute of Biomedical Imaging and Bioengineering (NIBIB) for funding. The use of the Rigaku/MSC microMax 007HF and Formulator in the Rockefeller University Structural Biology Resource Center was made possible by grant numbers 1S10RR022321-01 and 1S10RR027037-01 from the National Center for Research Resources of the NIH. We thank B. Black for sharing data before publication, A. Ruthenburg, J. Song and Z. Cheng for advice and discussions, and E. Datan for help in expressing DAXX protein. D.J.P. was supported by funds from the Abby Rockefeller Mauze Trust, and the Maloris and STARR Foundations. C.D.A. also acknowledges support from the STARR Foundation and The Rockefeller University. J.W.C. acknowledges support from UK Medical Research Council (MRC) (grants U105181009 and UD99999908). S.J.E. was supported by a Boehringer Ingelheim Funds fellowship and the David Rockefeller Graduate Program and holds an EMBO ALTF 1232-2011.

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Author notes

  1. Simon J. Elsässer and Hongda Huang: These authors contributed equally to this work.

Authors and Affiliations

  1. Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, 10065, New York, USA

    Simon J. Elsässer, Peter W. Lewis & C. David Allis

  2. MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK

    Simon J. Elsässer & Jason W. Chin

  3. Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, 10065, New York, USA

    Hongda Huang & Dinshaw J. Patel

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  1. Simon J. Elsässer
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  6. Dinshaw J. Patel
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Contributions

S.J.E. conceived and led the use of rigidifying mutants to crystallize the complex. Crystals of the seven- and five-substituent complexes were grown by S.J.E. and H.H., respectively. H.H. solved all the crystal structures of the complexes, including mutant complexes, under the supervision of D.J.P. S.J.E. performed biochemical and most cell-based experiments under the supervision of C.D.A and J.W.C. P.W.L carried out cell-based experiments and contributed reagents. All authors discussed the results and commented on the manuscript during its preparation.

Corresponding authors

Correspondence to C. David Allis or Dinshaw J. Patel.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-18 and Supplementary Tables 1 and 2. (PDF 17204 kb)

Video of DAXX-H3.3-H4 complex

Video of the ternary complex of DAXX (ribbon representation in magenta), H3.3 and H4 (surface representations in blue and green, respectively). The DAXX chaperone in an all alpha-helical conformation envelops the histone H3.3-H4 dimer for H3.3-specific recognition. (AVI 6541 kb)

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Elsässer, S., Huang, H., Lewis, P. et al. DAXX envelops a histone H3.3–H4 dimer for H3.3-specific recognition. Nature 491, 560–565 (2012). https://doi.org/10.1038/nature11608

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